|
| Status |
Public on Dec 05, 2017 |
| Title |
Hi-C_E6.5Epi_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Postimplantation embryo_E6.5 Epiblast
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6N x PWK/PhJ
developmental stage: E6.5
tissue: Epiblast
|
| Treatment protocol |
C57BL/6N female mice were induced for superovulation by injections of 5 IU of pregnant mare’s serum gonadotrophin and 5 IU of human chorionic gonadotrophin (44-48 hours apart) and mated to DBA/2N males.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
After trypsin and pancreatic enzyme digestion followed by mechanical dissection to separate epiblast and visceral endoderm, embryonic cells were washed with PBS and incubated in lysis buffer. Hi-C libraries were prepared using a protocol described in Du et al., Nature, 2017, 547(7662):232.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
Processed data file: Hi-C_processed_data_files.tar.gz.
|
| Data processing |
Basecalls were performed using CASAVA version 1.8.
Sequencing reads were mapped, processed and iteratively corrected using HiC-Pro, a pipeline developed by Servant et al. Briefly, the read pairs were mapped to the mm9 reference genome in a two-step approach with Bowtie2. Next, the invalid read pairs including dangling end, self-circle ligation and duplicates were discarded. The genome was divided into bins of specific length to generate the contact maps. For global detection of contacts, a 100Kb bin size was used and a 40Kb bin size was used for examination of local domain level contacts. The raw contact counts were normalized with iterative correction.
Genome build: mm9.
Processed data files format and content: The compartment files contain the values which indicate compartment A (more than 0) or compartment B (less than 0) in 100kb bin in the genome. The matrix txt file includes the interaction frequency between the two bins (represented by the number in the bed file) in first two columns. These files are available in a tar archive on the series record.
|
| |
|
| Submission date |
May 04, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Wei Xie |
| E-mail(s) |
xiewei121@tsinghua.edu.cn
|
| Organization name |
Tsinghua University
|
| Street address |
Zhongguancun north street
|
| City |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (1) |
| GSE76505 |
Dynamic epigenomic landscapes during early lineage specification in mouse embryos |
|
| Relations |
| BioSample |
SAMN04940130 |
| SRA |
SRX1741862 |
